Benthic, urchin, and fish observation data collected using multiple methodologies to calculate coral reef carbonate budget estimates for sites in the Mariana Archipelago in 2022 (NCEI Accession 0283896)
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title: Benthic, urchin, and fish observation data collected using multiple methodologies to calculate coral reef carbonate budget estimates for sites in the Mariana Archipelago in 2022 (NCEI Accession 0283896)
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abstract: This data package includes the benthic, urchin, and fish observation data collected for coral reef carbonate budget assessments by the Ecosystem Sciences Division (ESD) of NOAA's Pacific Island Fisheries Science Center (PIFSC) at fixed sites across the Mariana Archipelago in 2022. These data were collected as part of a three-year methods development and pilot project funded by the NOAA Coral Reef Conservation Program (CRCP) in order to establish a standardized carbonate budget methodology for the National Coral Reef Monitoring Program (NCRMP) in the U.S. Pacific Islands. Observational data were collected at the same sites using established Indo-Pacific ReefBudget methodology (Perry et al. 2018), as well as experimental methodologies that leverage existing NCRMP data streams (see the InPort record below for additional details on data collection methodologies). Benthic survey data (genus/species, morphology, and surface distance of corals, crustose coralline algae, macroalgae, and other benthic components) and urchin survey data (genus/species, test size, and abundance of bioeroding urchins) were collected using Indo-Pacific Reef Budget-style transects, "chords" transects located within the 12-m diameter circular footprint covered by NCRMP Structure-from-Motion imagery, and virtual transects in fixed site Structure-from-Motion models. Fish survey data (genus/species, count, and size) were collected using Indo-Pacific ReefBudget belt transects, stationary point count surveys conducted at fixed sites, and averaging stationary point count survey data using stratified random survey design around a set distance of the fixed sites. The raw data in this data package were utilized with referential databases to calculate coral reef carbonate budget estimates for Pacific regions. These databases can be found in the Documentation for this package; the two databases include a calcification rates referential database (developed & customized for the U.S. Pacific Islands region from the Indo-Pacific ReefBudget calcification rates database, accessible on the GitHub repository for this project: https://github.com/hannahbarkley/reefbudgetR/tree/main), as well as a referential database of grazing estimates for herbivorous fishes in Pacific Islands regions (already archived and documented as NCEI Accession 0259399). Other relevant scripts for producing carbonate budget estimates from raw data and referential data are also available on this project's GitHub repository.
purpose: Benthic, urchin, and fish observation data may be used to calculate site-level carbonate production and carbonate erosion rates. Coral reef framework is produced by the growth of corals, crustose coralline algae, and other benthic calcifiers, and persists when rates of carbonate production outpace rates of physical erosion from storms, chemical dissolution, and biological erosion from corallivorous fish, urchins, macrobioeroders, and microbioeroders. The relative rates of gross carbonate production and carbonate erosion and resulting net rate of carbonate production -- the reef's carbonate budget -- thus offer a quantitative metric for assessing coral reef functional status, growth potential, and capacity for maintaining complex habitat. Tracking these metrics becomes increasingly critical under a rapidly changing climate, as ocean warming, ocean acidification, and sea-level rise threaten to reduce rates of coral and crustose coralline algae calcification, accelerate rates of carbonate erosion, and thereby jeopardize the persistence of coral reef habitat. Pilot data collected using various methodologies in 2021 and 2022 were used to establish standard operating procedures for National Coral Reef Monitoring Program (NCRMP) carbonate budget assessments in the U.S. Pacific Islands. The NOAA National Coral Reef Monitoring Program (NCRMP) details a long term approach to provide an ecosystem perspective via monitoring climate, fish, benthic, and socioeconomic variables in a consistent and integrated manner. The NCRMP coordinates various NOAA Coral Reef Conservation Program (CRCP) biological, physical, and human dimensions activities into a cohesive NOAA-wide effort. Through the implementation of the NCRMP, NOAA is able to clearly and concisely communicate results of national-scale monitoring to national, state, and territorial policy makers, resource managers, and the public on a periodic basis. NCRMP is a framework for conducting sustained observations of biological, climate, and socioeconomic indicators at 10 priority coral reefs across the U.S. and its territories. This integrated approach consolidates monitoring of coral reefs under a uniform method in the Pacific, Atlantic, Caribbean, and the Gulf of Mexico for the first time. NCRMP is funded by the Coral Reef Conservation Program (CRCP) and supported by NOAA Fisheries, NOAA National Centers for Coastal Ocean Science (NCCOS), NOAA's Atlantic Oceanographic & Meteorological Laboratory (AOML), NOAA Coral Reef Watch, and many other partners. The Ecosystem Sciences Division (ESD) at NOAA Fisheries is leading in-situ climate monitoring in the U.S. Pacific Islands Region. The climate component of NCRMP in the Pacific provides a comprehensive view of climate change impacts on coral reef ecosystems and helps identify areas of resilience and vulnerability. The key indicators used to identify and monitor climate-driven trends include 1) thermal stress caused by changes in sea temperature, 2) ocean acidification resulting from changes in carbonate chemistry, and 3) ecological impacts by collecting data on coral growth rates, erosion, and community structure to understand the impacts of thermal stress and ocean acidification on the ecosystem. Each year, ESD scientists work closely with CRCP and partners during Reef Assessment and Monitoring Program (RAMP) missions to collect data using moored oceanographic and ecological instruments stationed at fixed sites in the Pacific Ocean, and water samples collected by divers. The in-situ data and satellite-based observations are also used in modeling efforts. Innovative analysis techniques are used to develop products that give fellow scientists, managers, decision makers and the public a better understanding of a region's resources and how they are changing over time.
credit: Related Funding Agency: US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center
credit: Related Funding Agency: US DOC; NOAA; NOS; Coral Reef Conservation Program
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title: NCEI Accession 0283896 v1.1
date: (CI_Date)
date: (inapplicable)
dateType: (CI_DateTypeCode) publication
citedResponsibleParty: (CI_ResponsibleParty)
individualName: (inapplicable)
contactInfo: (CI_Contact)
onlineResource: (CI_OnlineResource)
linkage: https://www.ncei.noaa.gov/archive/accession/0283896/1.1
protocol: HTTPS
name: NCEI Accession 0283896 v1.1
description: published 2023-10-20T16:02:38Z
function: (CI_OnLineFunctionCode) download
role: (inapplicable)
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dataQualityInfo: (DQ_DataQuality)
scope: (DQ_Scope)
level: (MD_ScopeCode) dataset
lineage: (LI_Lineage)
processStep: (LE_ProcessStep)
description: Parameter or Variable: SPECIES IDENTIFICATION (measured); Units: unitless; Observation Category: in situ; Sampling Instrument: swimmer/diver; Sampling and Analyzing Method: Benthic Indo-Pacific ReefBudget: Following Indo-Pacific ReefBudget methodology, benthic survey data were collected by divers along six 10-m transects per site. Transects were laid out in two parallel rows of three -- where the middle transects in each row were overlaid on the inshore and offshore 10-m edges of the fixed site box -- with 5-m spacing between adjacent transects. Along each transect, the surface cover (cm) of every benthic component located directly beneath the transect tape was measured with a flexible measuring tape. Data were collected on the following benthic components: hard coral (identified to genus/species and morphology), crustose coralline algae (CCA), macroalgae, turf, sand, carbonate hard substrate, non-carbonate hard substrate, or other (including cyanobacteria, soft coral, seagrass, sponges, zoanthids, corallimorphs, or other invertebrates). The surface cover of coral colonies with open branching morphologies (e.g. Acropora intermedia, Pocillopora grandis) was estimated by multiplying the total number of branches directly beneath the transect tape by the average branch diameter, and empty space between and beneath the live branches was considered to be turf. This approach minimizes potential over-estimation of live coral cover that can occur when draping the tape over an entire branching colony (where void space is included in the surface cover measurement). Surface cover of colonies with closed branching morphologies (e.g. Acropora humilis, Pocillopora damicornis; where void space between branches is minimal and all substrate beneath the transect tape is coral skeleton) was measured by draping the tape over the entire colony. Benthic Chords: Divers collected in-water benthic data along the same set of transects that were later surveyed virtually using SfM. To ensure that transects fell within the 12-m SfM circular footprint, a master transect tape was first established along the inshore, 10-m edge of the fixed site box. Six 8-m to 10-m perpendicular transects (2 x 8 m, 2 x 9 m, and 2 x 10 m) were then laid out at predetermined distances along the master transect tape with 1.5-m spacing between transects (shorter transects closer to the edges, longer transects towards the center of the circle). Benthic data were collected along the six perpendicular transects according to the Indo-Pacific ReefBudget methodology outlined above. Yellow dive weights were placed on the benthos at the beginning and end of each diver-completed transect; these weights were included in subsequent SfM imagery collection to mark the locations of diver-collected transects. Urchin Indo-Pacific ReefBudget: Urchin surveys were conducted over a 1 m-wide belt along the same transects used for Indo-Pacific ReefBudget benthic surveys. Along each transect, divers recorded the number and test size (size of the urchin shell excluding spines) for the following genera/species: Echinostrephus spp., Echinothrix spp., Diadema spp., Echinometra spp. (including Echinometra mathaei), and Parasalenia spp.. Test sizes were measured with a scale bar on the side of the dive slates and binned into 20 mm size classes: 0-20 mm, 21-40 mm, 41-60 mm, 61-80 mm, 81-100 mm, 101-120 mm, 121-140 mm, and 141-160 mm. Urchin Chords: urchin surveys (1 m x 8-10 m belt transects) were conducted along the same chords transects surveyed for the benthic methodology following the Indo-Pacific ReefBudget procedure. Fish Belt surveys: The belt method is used to conduct reef fish surveys around the Hawaiian Archipelago and the Marianas Archipelago as part of the carbonate budget pilot study. Fish are counted and sized (total length in centimeters, binned into 10cm size classes) along a 5 x 30 m transect area at ten different locations within 30m of a fixed site previously established by ESD's Ocean and Climate Change team. The belt method catalogs the density (abundance per hectare), biomass (kg per hectare), and bioerosion (kilograms per meters squared per year) of diurnally active reef fish assemblages in shallow-water (average 15m) hard-bottom habitats. Bioerosion metrics are calculated using foraging metrics that have been derived from literature where Pacific fish species were prioritized. These three values include: 1) proportion of bites leaving scars, 2) bite rates (bites per minute), and 3) volume removed per bite (centimeters cubed). Fish Stationary Point Count surveys: The stationary point count (SPC) method is used to conduct reef fish surveys as part of the NOAA National Coral Reef Monitoring Program (NCRMP). The SPC method catalogs the diversity (species richness), abundance (numeric density) and biomass (fish mass per unit area) of diurnally active reef fish assemblages in shallow-water (less than 30 m) hard-bottom habitats. This study uses two complimentary sampling designs to survey the coral reef ecosystems at and around selected fixed-sites: 1) A stratified random sampling (StRS) design and 2) a fixed-site (fixed SPC) sampling design. The StRS survey domain encompasses the majority of the mapped area of reef and hard bottom habitats within 12.5 km of permanent fixed-sites previously established by ESD's Ocean and Climate Change team. The stratification includes island, reef zone, depth, and habitat structure type. Sampling effort is anywhere between 16 to 55 StRS SPC sites within 12.5 kilometers of each fixed-site, excluding the fixed SPC data.; Data Quality Method: The same methods of data collection are used at each surveyed site. Observations at each site were made by divers who have been trained, and met minimum standards in identifying species present at the survey locations and in estimating size of benthic, urchin, and fish. All species identifications are made visually. Observations, including species identification and sizing, are periodically checked during expeditions for consistency between divers (diver bias) or other discrepancies. Data entry is usually conducted on the same day as the surveys using a data entry interface with several data controls employed, and are quality controlled by the divers using a two-person system. Following a mission, the data is then run through rigorous quality control checks by the data management team before the data are migrated to the Oracle database. Given the size of the data set, there remains some possibility of typographical or other errors..
processStep: (LE_ProcessStep)
description: Parameter or Variable: SPECIES IDENTIFICATION - ORGANISM LENGTH (measured); Units: centimeter; Observation Category: in situ; Sampling Instrument: swimmer/diver; Sampling and Analyzing Method: Urchin Indo-Pacific ReefBudget: Urchin surveys were conducted over a 1 m-wide belt along the same transects used for Indo-Pacific ReefBudget benthic surveys. Along each transect, divers recorded the number and test size (size of the urchin shell excluding spines) for the following genera/species: Echinostrephus spp., Echinothrix spp., Diadema spp., Echinometra spp. (including Echinometra mathaei), and Parasalenia spp.. Test sizes were measured with a scale bar on the side of the dive slates and binned into 20 mm size classes: 0-20 mm, 21-40 mm, 41-60 mm, 61-80 mm, 81-100 mm, 101-120 mm, 121-140 mm, and 141-160 mm. Urchin Chords: urchin surveys (1 m x 8-10 m belt transects) were conducted along the same chords transects surveyed for the benthic methodology following the Indo-Pacific ReefBudget procedure. Fish Belt surveys: The belt method is used to conduct reef fish surveys around the Hawaiian Archipelago and the Marianas Archipelago as part of the carbonate budget pilot study. Fish are counted and sized (total length in centimeters, binned into 10cm size classes) along a 5 x 30 m transect area at ten different locations within 30m of a fixed site previously established by ESD's Ocean and Climate Change team. The belt method catalogs the density (abundance per hectare), biomass (kg per hectare), and bioerosion (kilograms per meters squared per year) of diurnally active reef fish assemblages in shallow-water (average 15m) hard-bottom habitats. Bioerosion metrics are calculated using foraging metrics that have been derived from literature where Pacific fish species were prioritized. These three values include: 1) proportion of bites leaving scars, 2) bite rates (bites per minute), and 3) volume removed per bite (centimeters cubed). Fish Stationary Point Count surveys: The stationary point count (SPC) method is used to conduct reef fish surveys as part of the NOAA National Coral Reef Monitoring Program (NCRMP). The SPC method catalogs the diversity (species richness), abundance (numeric density) and biomass (fish mass per unit area) of diurnally active reef fish assemblages in shallow-water (less than 30 m) hard-bottom habitats. This study uses two complimentary sampling designs to survey the coral reef ecosystems at and around selected fixed-sites: 1) A stratified random sampling (StRS) design and 2) a fixed-site (fixed SPC) sampling design. The StRS survey domain encompasses the majority of the mapped area of reef and hard bottom habitats within 12.5 km of permanent fixed-sites previously established by ESD's Ocean and Climate Change team. The stratification includes island, reef zone, depth, and habitat structure type. Sampling effort is anywhere between 16 to 55 StRS SPC sites within 12.5 kilometers of each fixed-site, excluding the fixed SPC data.; Data Quality Method: The same methods of data collection are used at each surveyed site. Observations at each site were made by divers who have been trained, and met minimum standards in identifying species present at the survey locations and in estimating size of urchin and fish. All species identifications are made visually. Observations, including species identification and sizing, are periodically checked during expeditions for consistency between divers (diver bias) or other discrepancies. Data entry is usually conducted on the same day as the surveys using a data entry interface with several data controls employed, and are quality controlled by the divers using a two-person system. Following a mission, the data is then run through rigorous quality control checks by the data management team before the data are migrated to the Oracle database. Given the size of the data set, there remains some possibility of typographical or other errors..
processStep: (LE_ProcessStep)
description: Parameter or Variable: REEF AND/OR BOTTOM REGIME - PERCENT COVER (measured); Units: percent; Observation Category: in situ; Sampling Instrument: swimmer/diver; Sampling and Analyzing Method: Fish Stationary Point Count surveys: On completing the fish count, divers make rapid visual estimates of benthic cover and structural complexity of the substrate within their survey cylinder. Benthic cover is estimated for broad functional groups (e.g., hard coral, sand, macroalgae). Structural complexity is determined by estimating the amount of the cylinder within 5 substrate-height bins (<20 cm, 20-50 cm; 50-100 cm; 100-150 cm, and >150 cm).; Data Quality Method: Visual estimates of benthic cover are useful as broad indication of the reef benthic assemblages present at each survey site, but there is considerable scope for error in rapid diver estimates of this kind..
processStep: (LE_ProcessStep)
description: Parameter or Variable: MACROINVERTEBRATE CENSUS (measured); Units: unitless; Observation Category: in situ; Sampling Instrument: swimmer/diver; Sampling and Analyzing Method: Urchin Indo-Pacific ReefBudget: Urchin surveys were conducted over a 1 m-wide belt along the same transects used for Indo-Pacific ReefBudget benthic surveys. Along each transect, divers recorded the number and test size (size of the urchin shell excluding spines) for the following genera/species: Echinostrephus spp., Echinothrix spp., Diadema spp., Echinometra spp. (including Echinometra mathaei), and Parasalenia spp.. Test sizes were measured with a scale bar on the side of the dive slates and binned into 20 mm size classes: 0-20 mm, 21-40 mm, 41-60 mm, 61-80 mm, 81-100 mm, 101-120 mm, 121-140 mm, and 141-160 mm. Urchin Chords: urchin surveys (1 m x 8-10 m belt transects) were conducted along the same chords transects surveyed for the benthic methodology following the Indo-Pacific ReefBudget procedure. Fish Stationary Point Count Surveys: Urchin and boring urchin categorized as dominant (D), abundant (A), common (C), occasional (O), or rare (R); Data Quality Method: The same methods of data collection are used at each surveyed site. Observations at each site were made by divers who have been trained, and met minimum standards in identifying species present at the survey locations and in estimating size of urchins. All species identifications are made visually. Observations, including species identification and sizing, are periodically checked during expeditions for consistency between divers (diver bias) or other discrepancies. Data entry is usually conducted on the same day as the surveys using a data entry interface with several data controls employed, and are quality controlled by the divers using a two-person system. Following a mission, the data is then run through rigorous quality control checks by the data management team before the data are migrated to the Oracle database. Given the size of the data set, there remains some possibility of typographical or other errors..
processStep: (LE_ProcessStep)
description: Parameter or Variable: REEF AND/OR BOTTOM REGIME - SURFACE AREA (measured); Units: centimeter; Observation Category: in situ; Sampling Instrument: swimmer/diver; Sampling and Analyzing Method: Benthic Indo-Pacific ReefBudget: Following Indo-Pacific ReefBudget methodology, benthic survey data were collected by divers along six 10-m transects per site. Transects were laid out in two parallel rows of three -- where the middle transects in each row were overlaid on the inshore and offshore 10-m edges of the fixed site box -- with 5-m spacing between adjacent transects. Along each transect, the surface cover (cm) of every benthic component located directly beneath the transect tape was measured with a flexible measuring tape. Data were collected on the following benthic components: hard coral (identified to genus/species and morphology), crustose coralline algae (CCA), macroalgae, turf, sand, carbonate hard substrate, non-carbonate hard substrate, or other (including cyanobacteria, soft coral, seagrass, sponges, zoanthids, corallimorphs, or other invertebrates). The surface cover of coral colonies with open branching morphologies (e.g. Acropora intermedia, Pocillopora grandis) was estimated by multiplying the total number of branches directly beneath the transect tape by the average branch diameter, and empty space between and beneath the live branches was considered to be turf. This approach minimizes potential over-estimation of live coral cover that can occur when draping the tape over an entire branching colony (where void space is included in the surface cover measurement). Surface cover of colonies with closed branching morphologies (e.g. Acropora humilis, Pocillopora damicornis; where void space between branches is minimal and all substrate beneath the transect tape is coral skeleton) was measured by draping the tape over the entire colony. Benthic Chords: Divers collected in-water benthic data along the same set of transects that were later surveyed virtually using SfM. To ensure that transects fell within the 12-m SfM circular footprint, a master transect tape was first established along the inshore, 10-m edge of the fixed site box. Six 8-m to 10-m perpendicular transects (2 x 8 m, 2 x 9 m, and 2 x 10 m) were then laid out at predetermined distances along the master transect tape with 1.5-m spacing between transects (shorter transects closer to the edges, longer transects towards the center of the circle). Benthic data were collected along the six perpendicular transects according to the Indo-Pacific ReefBudget methodology outlined above. Yellow dive weights were placed on the benthos at the beginning and end of each diver-completed transect; these weights were included in subsequent SfM imagery collection to mark the locations of diver-collected transects.; Data Quality Method: The same methods of data collection are used at each surveyed site. Observations at each site were made by divers who have been trained, and met minimum standards in identifying species present at the survey locations and in estimating size of benthic organisms. All species identifications are made visually. Observations, including species identification and sizing, are periodically checked during expeditions for consistency between divers (diver bias) or other discrepancies. Data entry is usually conducted on the same day as the surveys using a data entry interface with several data controls employed, and are quality controlled by the divers using a two-person system. Following a mission, the data is then run through rigorous quality control checks by the data management team before the data are migrated to the Oracle database. Given the size of the data set, there remains some possibility of typographical or other errors..
processStep: (LE_ProcessStep)
description: Parameter or Variable: SPECIES IDENTIFICATION (measured); Units: unitless; Observation Category: laboratory analysis; Sampling Instrument: visual observation; Sampling and Analyzing Method: Structure-from-Motion: Benthic data collection makes use of fixed-site SfM imagery already collected as part of NCRMP monitoring efforts. Imagery was collected at each site following NCRMP standard operating procedures (Rodriguez et al. 2021). The images were processed with Agisoft Metashape photogrammetry software to produce a scaled digital elevation model (DEM) and corresponding orthomosaic for each site. Benthic data were extracted from these two high resolution reef models in ArcGIS Pro 3.0.3 using a customized tool that replicates in-water benthic data collection in the SfM environment. Structure-from-Motion: Extraction of urchin data from SfM imagery was conducted for Oahu sites using ArcGIS Pro and NOAA Video and Image Analytics for Marine Environments (VIAME) software. In ArcGIS Pro, virtual benthic transects laid in each fixed-site orthomosaic were cropped to the extent of the belt transect survey area (1 m x 8-10 m) and exported as individual jpeg images for each transect. Belt transect images were then uploaded to VIAME, and all visible urchins in were identified to genus/species and sized with a bounding box. The total length of each urchin (length of the test plus spines) was estimated to be the largest dimension of the bounding box..
processStep: (LE_ProcessStep)
description: Parameter or Variable: SPECIES IDENTIFICATION - ORGANISM LENGTH (measured); Units: centimeter; Observation Category: laboratory analysis; Sampling Instrument: visual observation; Sampling and Analyzing Method: Urchin Structure-from-Motion: Extraction of urchin data from SfM imagery was conducted for Oahu sites using ArcGIS Pro and NOAA Video and Image Analytics for Marine Environments (VIAME) software. In ArcGIS Pro, virtual benthic transects laid in each fixed-site orthomosaic were cropped to the extent of the belt transect survey area (1 m x 8-10 m) and exported as individual jpeg images for each transect. Belt transect images were then uploaded to VIAME, and all visible urchins in were identified to genus/species and sized with a bounding box. The total length of each urchin (length of the test plus spines) was estimated to be the largest dimension of the bounding box..
processStep: (LE_ProcessStep)
description: Parameter or Variable: REEF AND/OR BOTTOM REGIME - SURFACE AREA (measured); Units: centimeter; Observation Category: laboratory analysis; Sampling Instrument: visual observation; Sampling and Analyzing Method: Structure-from-Motion: Benthic data collection makes use of fixed-site SfM imagery already collected as part of NCRMP monitoring efforts. Imagery was collected at each site following NCRMP standard operating procedures (Rodriguez et al. 2021). The images were processed with Agisoft Metashape photogrammetry software to produce a scaled digital elevation model (DEM) and corresponding orthomosaic for each site. Benthic data were extracted from these two high resolution reef models in ArcGIS Pro 3.0.3 using a customized tool that replicates in-water benthic data collection in the SfM environment..
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metadataMaintenance: (MD_MaintenanceInformation)
maintenanceAndUpdateFrequency: (MD_MaintenanceFrequencyCode) asNeeded
maintenanceNote: Metadata are developed, maintained and distributed by NCEI. Updates are performed as needed to maintain currentness.
contact: (CI_ResponsibleParty)
organisationName: NOAA National Centers for Environmental Information
role: (CI_RoleCode) custodian
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acquisitionInformation: (MI_AcquisitionInformation)
instrument: (MI_Instrument)
identifier: (MD_Identifier)
code: swimmer/diver
type: swimmer/diver
description: not an instrument - use as observation type
instrument: (MI_Instrument)
identifier: (MD_Identifier)
code: visual observation
type: visual observation
description: not an instrument - maybe an observation type
platform: (MI_Platform)
identifier: (MD_Identifier)
code: NOAA Ship Rainier
description: Title: NOAA Ship Flag: United States of America Vessel Type: Research Vessel (Hydrographic) DOB: Apr 1968 IMO: 6711003 Hull Classification: S 221
instrument: (missing)
